InfiniumPurify {InfiniumPurify}

Purify tumor methylomes caused by normal cell contamination.

Description

Deconvolute purified tumor methylomes accounting for tumor purity.

Usage

InfiniumPurify(tumor.data,normal.data,purity)

Arguments

tumor.data

numeric matrix of beta values for tumor samlpes. The rownames of tumor.data should be probe names of Infinium 450k array, and colnames should be names of tumor samples.

normal.data

numeric matrix of beta values for normal samlpes. The rownames of normal.data should be probe names of Infinium 450k array, and colnames should be names of normal samples.

purity

purities for tumor samples. Could be estimated by getPurity, or user specified purities from other tools.

Details

The function deconvolutes purified tumor methylomes by a linear regression model.

Value

A matrix of purified beta values for all CpG sites (row) and tumor samples (column).

Author(s)

Xiaoqi Zheng [e-mail].

References

X. Zheng, N. Zhang, H.J. Wu and H. Wu, Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies. Genome biology, accepted.

Examples

## load example data
data(beta.emp)

normal.data <- beta.emp[,1:21]
tumor.data <- beta.emp[,22:61]

## estimate tumor purity
purity <- getPurity(tumor.data = tumor.data,normal.data = NULL,tumor.type= "LUAD")

## correct tumor methylome by tumor purity
tumor.purified = InfiniumPurify(tumor.data = tumor.data[1:100,],
                                normal.data = normal.data[1:100,],
                                purity = purity)